Contacts of the helix formed by residues 156 - 171 (chain B) in PDB entry 3E61
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B THR* 1.3 76.3 - - - +
157B HIS* 1.3 61.2 + - - +
158B PHE* 3.4 14.2 - - - +
159B LYS* 3.0 36.7 + - + +
160B GLY* 3.0 22.7 + - - -
190B GLN* 4.4 10.1 + - - -
263B TYR* 5.0 0.2 - - - -
311B LEU* 3.8 7.9 - - + +
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Residues in contact with HIS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B GOL 3.9 18.4 - - - -
144B ASP* 3.8 21.3 + - + -
154B SER* 3.1 28.3 + - - -
155B THR* 3.8 6.7 + - - -
156B ASN* 1.3 73.9 - - - +
158B PHE* 1.3 60.1 + - - +
160B GLY* 3.3 1.7 + - - +
161B GLY 3.0 23.4 + - - -
187B ALA* 3.5 41.3 - - + +
190B GLN* 3.8 23.5 + - + -
191B ARG* 3.2 29.8 + - + +
263B TYR* 4.5 6.9 + - - -
281B GLN* 4.1 9.5 + - - -
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ASN* 3.3 14.5 + - - +
157B HIS* 1.3 78.3 - - - +
159B LYS* 1.3 61.1 + - - +
161B GLY 3.3 0.5 + - - -
162B GLN* 3.1 54.6 + - + +
190B GLN* 3.5 25.7 + - + +
193B GLN* 3.5 30.5 - - + -
194B GLY* 3.2 22.3 - - - -
197B TYR* 3.8 20.2 - - + -
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ASN* 3.0 28.2 + - + +
158B PHE* 1.3 75.1 - - - +
160B GLY* 1.3 64.7 + - - +
162B GLN* 3.2 20.9 + - - +
163B LEU* 3.1 28.1 + - + +
311B LEU* 4.5 8.3 - - + -
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Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ASN 3.0 11.5 + - - -
157B HIS 3.3 1.3 + - - -
158B PHE 3.3 0.4 - - - -
159B LYS* 1.3 76.8 - - - +
161B GLY* 1.3 60.9 + - - +
163B LEU* 3.2 11.2 + - - +
164B GLN* 3.1 24.8 + - - +
263B TYR* 3.1 35.6 - - - -
311B LEU* 3.8 8.6 - - - +
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Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B HIS 3.0 11.7 + - - -
158B PHE 3.3 1.5 + - - -
159B LYS 3.3 0.2 - - - -
160B GLY* 1.3 72.0 - - - +
162B GLN* 1.3 65.1 + - - +
164B GLN* 3.3 7.0 + - - -
165B ALA 3.1 17.7 + - - -
191B ARG* 3.3 34.8 - - - +
195B ILE* 3.4 20.3 - - - +
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Residues in contact with GLN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PHE* 3.1 45.6 + - + +
159B LYS* 3.2 18.2 + - - +
161B GLY* 1.3 74.6 - - - +
163B LEU* 1.3 60.4 + - + +
165B ALA* 3.3 2.9 + - - +
166B GLU* 3.0 29.0 + - - +
194B GLY* 3.6 15.7 - - - +
197B TYR* 4.8 2.7 - - + -
198B ILE* 3.7 33.8 - - + +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LYS* 3.1 15.8 + - + +
160B GLY* 3.3 10.1 - - - +
161B GLY 3.2 0.2 - - - -
162B GLN* 1.3 76.3 - - + +
164B GLN* 1.3 63.7 + - - +
166B GLU* 3.8 8.0 - - + +
167B VAL* 3.3 28.4 + - - +
279B ILE* 3.8 16.8 - - + -
311B LEU* 4.0 39.9 - - + +
313B VAL* 4.1 23.5 - - + +
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Residues in contact with GLN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLY 3.1 14.7 + - - +
161B GLY* 3.5 7.5 - - - +
163B LEU* 1.3 78.2 - - - +
165B ALA* 1.3 61.0 + - - +
167B VAL* 3.4 6.4 + - - +
168B VAL* 3.3 23.4 + - - +
191B ARG* 3.6 23.8 - - - +
195B ILE* 3.6 8.9 - - + +
233B ILE* 3.4 29.5 - - + +
234B CYS 2.7 29.0 + - - +
235B SER* 5.3 0.3 - - - -
261B ILE* 3.9 16.3 + - + +
262B GLY 2.9 23.0 + - - +
263B TYR* 3.7 17.6 - - + -
279B ILE* 4.1 7.2 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B GLY 3.1 12.2 + - - +
162B GLN 3.3 1.1 + - - +
164B GLN* 1.3 77.0 - - - +
166B GLU* 1.3 60.3 + - - +
168B VAL* 3.3 5.7 + - - +
169B ARG* 2.8 27.0 + - - +
195B ILE* 3.7 20.6 - - + +
198B ILE* 3.6 31.7 - - + +
199B LEU* 4.1 12.4 - - + +
233B ILE* 4.0 10.0 - - - +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLN 3.0 17.4 + - - +
163B LEU* 3.8 10.8 - - + +
164B GLN 3.3 0.2 - - - -
165B ALA* 1.3 73.5 - - - +
167B VAL* 1.3 60.7 + - - +
169B ARG* 3.1 11.5 + - - +
170B LYS* 2.9 51.1 + - + +
198B ILE* 4.3 8.0 - - + +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU 3.3 13.6 + - - +
164B GLN 3.6 8.1 - - - +
166B GLU* 1.3 76.7 - - + +
168B VAL* 1.3 58.7 + - - +
170B LYS* 3.3 10.0 + - - +
171B GLY* 3.0 24.6 + - - -
259B GLN* 4.5 1.2 + - - +
261B ILE* 3.7 15.3 - - + -
277B THR* 4.2 4.7 - - + -
313B VAL* 3.6 32.1 - - + -
315B HIS* 4.0 16.4 - - + +
319B THR* 3.6 35.2 - - + +
320B ARG 5.0 2.2 - - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLN 3.3 8.3 + - - +
165B ALA* 3.5 10.3 - - - +
166B GLU 3.2 0.4 - - - -
167B VAL* 1.3 75.2 - - + +
169B ARG* 1.3 66.8 + - - +
171B GLY 3.1 7.1 + - - -
173B GLY* 3.0 26.0 + - - -
176B VAL* 3.8 24.0 - - + -
199B LEU* 4.7 7.2 - - + -
204B ILE* 5.4 0.4 - - + -
231B SER* 3.8 23.3 - - - +
232B ILE 5.4 1.1 - - - +
233B ILE* 3.6 28.7 - - + -
259B GLN* 3.3 18.5 + - + +
261B ILE* 4.1 10.3 - - + -
319B THR* 5.7 0.7 - - + -
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ALA 2.8 16.3 + - - +
166B GLU* 3.1 12.2 + - - +
168B VAL* 1.3 73.6 - - - +
170B LYS* 1.3 92.3 + - - +
172B LYS* 3.0 21.7 + - - +
173B GLY 4.6 1.1 - - - +
198B ILE* 5.0 7.3 - - + +
202B GLN* 3.4 44.8 - - + +
204B ILE* 4.3 19.5 - - + -
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLU* 2.9 38.8 + - - +
167B VAL* 3.7 10.1 - - - +
169B ARG* 1.3 105.8 - - - +
171B GLY* 1.3 56.8 - - - +
172B LYS* 3.0 16.9 + - - +
315B HIS* 5.8 7.6 - - - -
320B ARG 4.6 4.8 - - - +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B VAL 3.0 11.1 + - - -
168B VAL 3.1 5.1 + - - -
170B LYS* 1.3 73.3 - - - +
172B LYS* 1.3 66.4 + - - +
173B GLY 3.4 2.2 - - - -
259B GLN* 3.6 17.9 - - - -
320B ARG* 2.8 50.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il